Deploy shiny on aws

I recently want to deploy my intern company’s R shiny on aws so that everyone can use it. I googled some tutorials but some of them is outdataed, so I just want to write one to document it. (Just in case I need to deploy shiny again in the future).

I’m pretty new to this field, happy to disscuss.

I mainly used tutorial from here: https://tm3.ghost.io/2017/12/31/deploying-an-r-shiny-app-to-aws/

https://www.digitalocean.com/community/tutorials/how-to-install-r-on-ubuntu-18-04

https://www.linode.com/docs/development/r/how-to-deploy-rshiny-server-on-ubuntu-and-debian/

https://www.rstudio.com/products/rstudio/download-server/

Today I will go over xxxx things:

• Create an instance on aws
• Deploy a sample R shiny on aws
• Set up username and password when login the shiny

Step 1: Create an instance on aws

If you are a student, you can google aws student and sign up there by using your edu email to get some credits. Here, I assume you already have the account.

Click on the EC2 button, then Launch Instance, it will lead you to choose AMI page. Select the newest Unbuntu Server.

Then you goes to Step 2: Choose an Instance Type, here I choose t2.medium since it has 4GB memory, you can choose your own depends on you need. I also tried t2.micro, it’s too small so that I can’t even install R packages. Check this link to select the instance type you need: https://aws.amazon.com/ec2/instance-types/. Then click Next: Configure Instance Details. Don’t click Review and Launch.

Leave the Step 3: Configure Instance Details as it is, and click Next: Add Storage.

Change Size (GiB) to 16GB as recommend by some R bloggers. Click Next: Add Tags.

Click Add tag and type the name under the key. Here, mine is sample_shiny. Next, click Next: Configure Security Group.

This section is really important. It allows users to access the r studio and the shiny. Please choose the configuration as specified below. Then click Review and Launch.

Almost done!!! Click the Launch button and choose Create a new key pair. Type in the key name you want, mine is sample_shiny. Then click Download key pair and save the download file in a folder you want. As a demonstration, I saved mine on Desktop, you should save it to a more secure location just in case you won’t accidentally delete it. After you down, you should see a file named your_key_name.pem in your specified folder location. Lastly, click Launch Instances.

If you see this “Your instances are now launching”, that means you are good to go. Click on the Instance ID in the red box.

Connect to instance by clicking Connect and you should see a window pops up that tells you how to access your instance. Open your terminal on your laptop; I use the Terminal app on Mac. cd to the folder that store the key you just downloaded; mine is in Desktop.

Copy and paste the commnad line from step 3 in popped up window to terminal.

Mine is chmod 400 sample_shiny.pem.

Copy and paste ssh -i "sample_shiny.pem" ubuntu@yourpublicDNS to terminal. You can find this from Example in popped up window.

Type yes to Are you sure you want to continue connecting (yes/no)?.

If you see something like ubuntu@xxx, you are connected.

Step 2: Install system libraries, R, R studio server, R shiny server.

From your terminal you just logged in.

I. Install system required libraries.

$ sudo apt-get update
$ sudo apt-get -y install \
    nginx \
    gdebi-core \
    apache2-utils \
    pandoc \
    pandoc-citeproc \
    libssl-dev \
    libcurl4-gnutls-dev \
    libcairo2-dev \
    libgdal-dev \
    libgeos-dev \
    libproj-dev \
    libxml2-dev \
    libxt-dev \
    libv8-dev

II. Install R to ubuntu 18.04.

Follow this link: https://www.digitalocean.com/community/tutorials/how-to-install-r-on-ubuntu-18-04 Remeber if your ubuntu is not 18.04, you probably need to google the newest installation code.

$ sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
$ sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'
$ sudo apt update
$ sudo apt install r-base

If your R is succefully installed, then R will show up if you type sudo -i R. Here mine R is 3.6.1 (2019-07-05). Your version can be different than mine.

III. Install Shiny Server

Follow install shiny server from this link: https://www.linode.com/docs/development/r/how-to-deploy-rshiny-server-on-ubuntu-and-debian/

You should see something like this:

### Install gdebi
sudo apt install gdebi-core

### Download Shiny Server
wget https://download3.rstudio.org/ubuntu-12.04/x86_64/shiny-server-1.5.6.875-amd64.deb

Type y to Do you want to install the software package? [y/N]: If your shiny server is succesfully installed and running, you should see: Active: active (running).

### Use gdebi to install the Shiny Server package
sudo gdebi shiny-server-1.5.6.875-amd64.deb

### The shiny-server service should start automatically. Check its status
sudo systemctl status shiny-server.service

IV. Install R studio Server

Follow install R studio server from this link: https://www.rstudio.com/products/rstudio/download-server/

Choose the one based on your ubuntu version. Probably need to change something if your ubuntu is not 18.04.

You should see something like this:

$ sudo apt-get install gdebi-core
$ wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.2.1335-amd64.deb
$ sudo gdebi rstudio-server-1.2.1335-amd64.deb

Answer y to Do you want to install the software package? [y/N]:

If R studio server is running, you should see Active: active (running)

Step 2: Deploy R shiny

V. Install R Libraries

Install the libraries you need, may talk a while to run.

$ sudo su - -c "R -e \"install.packages(c('shiny', 'rmarkdown', 'shinydashboard', 'shinyjs'), repos='http://cran.rstudio.com/')\""

$ sudo su - -c "R -e \"install.packages(c('ggplot2', 'dplyr', 'tidyr', 'readr', 'lazyeval', 'stringr', 'ggthemes', 'ggExtra', 'magrittr', 'viridis', 'gridExtra', 'lubridate', 'fasttime', 'data.table'), repos='http://cran.rstudio.com/')\""

VI. Change configuration files

Back in terminal, stop the nginx service and the shiny-server.

$ sudo service nginx stop
$ sudo stop shiny-server

Change R Studio Config:

$ sudo vi /etc/nginx/sites-available/default

You will see something like this. Comment everything in this file. Everythinggggg !!!!!! Type i to enter insert mode and use # to comment.

Copy and paste the following to the file:

server {
    listen 80;

    location / {
    proxy_pass http://127.0.0.1:3838/;
    proxy_redirect http://127.0.0.1:3838/ $scheme://$host/;
    proxy_http_version 1.1;
    proxy_set_header Upgrade $http_upgrade;
    proxy_set_header Connection "upgrade";
    auth_basic "Username and Password are required";
    auth_basic_user_file /etc/nginx/.htpasswd;
 }
}

Use esc to exsit insert mode, type :wq to save and quit.

Change R Shiny Config:

$ sudo vi /etc/shiny-server/shiny-server.conf

Type i to enter insert mode and use # to comment.

Copy and paste the following to the file:

# Instruct Shiny Server to run applications as the user "shiny"
run_as shiny;

# Define a server that listens on port 3838
server {
  listen 3838;

  # Define a location at the base URL
  location / {

    # Host the directory of Shiny Apps stored in this directory
    site_dir /srv/shiny-server;

    # Log all Shiny output to files in this directory
    log_dir /var/log/shiny-server;

    # When a user visits the base URL rather than a particular application,
    # an index of the applications available in this directory will be shown.
    directory_index on;
  }
}

Use esc to exsit insert mode, type :wq to save and quit.

VII. Password Protecting the shiny App

If you don’t want everyone to access your shiny, you can set password to protect it. Here, I set name as Crystal. Enter the password.

$ cd /etc/nginx
$ sudo htpasswd -c /etc/nginx/.htpasswd Crystal

Add more users. You need to leave out the -c argument for any additional users you wish to add.

$ sudo htpasswd /etc/nginx/.htpasswd Newuser

VIII. Password Protecting the R studio

Start nginx and shiny:

$ sudo systemctl start shiny-server
$ sudo service nginx start

The login name is ubuntu, change the password:

$ sudo passwd ubuntu

Resart nginx and shiny:

$ sudo systemctl restart shiny-server
$ sudo service nginx restart

Now, your shiny server and studio server should work. Open your broswer, type IPv4 Public IP:8787, login with username ubuntu and password, you should then see the R studio server. The IPv4 Public IP is your ip address.

Type IPv4 Public IP:3838 login with username and password you just created, you should see something like this. The IPv4 Public IP is your ip address.

Step 3: Deploy shiny

In this tutorial, I already upload my shiny code to github, called deploy_shiny_sample https://github.com/JiaxuanZhao/deploy_shiny_sample. The code comes from one of the shiny tutorial.

Now back to terminal,

$ cd /srv/shiny-server
$ ls

You should see one index.html and one sample-apps

## Having problems with file permissions? 
$ sudo chmod 7777 /srv/shiny-server/

## install git
$ sudo apt-get install git

Back to github, clone the deploy_shiny_sample repo using the “Clone with HTTPS” url:

$ git clone https://github.com/JiaxuanZhao/deploy_shiny_sample.git
$ ls

You should see an extra folder called deploy_shiny_sample.

Restart nginx and shiny:

$ sudo systemctl restart shiny-server
$ sudo service nginx restart

In the web broswer, type IPv4 Public IP/deploy_shiny_sample, now you can see your shiny app.